Probing the druggability of the Notch1 ankyrin domain using a fragment-based approach

Abstract:

Notch signalling is a highly conserved pathway that is important in the developmental processes that control cell differentiation and cell fates. This canonical pathway involves binding of a transmembrane ligand in one cell to the extraceullular domain of a transmembrane Notch receptor in an adjacent cell.
Ligand binding triggers two sequential proteolytic cleavages that shed a Notch intracellular domain (NICD). This is followed by translocation of NICD to the
nucleus where it interacts with a transcription factor CSL and forms an activated Notch transcription complex, which induces the transcription of Notch target genes.
Abnormal expression or mutations in the different components of the pathway are associated with a number of diseases and cancers. An enhanced activity of
Notch signalling resulting from a mutation in the extracellular domain is implicated in the progression of T-acute lymphoblastic leukaemia (T-ALL).
Several therapeutic agents have been developed to target the Notch signalling pathway such as, γ-secretase inhibitors, antibodies targeting different regions of
the Notch receptor and recently a synthetic stapled peptide, which was found to inhibit the formation of the transcription complex. The current inhibitors have
their own disadvantages including lack of selectivity, cost of goods and delivery to the target. Thus, a more selective approach to target downstream proteinprotein
interactions by small molecules would provide an attractive approach to the design of new therapeutic agents that target this pathway. Here I report a
fragment-based approach to target the ankyrin domain, a historically known but challenging, often-considered “undruggable” target.
In this dissertation I describe the application of various biophysical and computational approaches to find, characterise and design compounds. The
initial screening of a commercial fragment-library exploited a fluorescent-based thermal shift assay that identified 36 fragment hits. Some of the fragments were
kinetically characterised by Surface Plasmon Resonance (SPR) and their affinities were found to be in the millimolar range. Several attempts at soaking
vii and co-crystallising the fragments in the ankyrin domain crystal resulted in only two successful crystal structures that clearly define the positions of the
fragments and their interactions with the ankyrin domain. One fragment binds to a pre-defined hotspot residue at the interface between the ankyrin domain and
CSL. The other fragment is located at the interface between the ankyrin domain and Mastermind (MAML). The structural and kinetic data assisted the design of
larger compounds with more extensive interactions using drug design software such as SPROUT and a docking program (GOLD). However, the optimised fragments did not show much improvement in affinity underlying the difficulty of flat protein-protein interface. The results reported here show the first structures of small molecules binding to the ankyrin domain of Notch1 receptor.